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- PDB-6hqa: Molecular structure of promoter-bound yeast TFIID -

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Basic information

Entry
Database: PDB / ID: 6hqa
TitleMolecular structure of promoter-bound yeast TFIID
Components
  • (Histone-fold) x 2
  • Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
  • Subunit (60 kDa) of TFIID and SAGA complexes
  • Subunit (61/68 kDa) of TFIID and SAGA complexes
  • Subunit (90 kDa) of TFIID and SAGA complexes
  • TFIID subunit (48 kDa)Transcription factor II D
  • Taf2
  • Taf8
KeywordsTRANSCRIPTION / Complex / Transcription initiation
Function / homology
Function and homology information


regulation of cellular biosynthetic process / regulation of primary metabolic process / positive regulation of DNA-templated transcription initiation / SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA polymerase II preinitiation complex assembly / DNA-templated transcription initiation / chromatin organization ...regulation of cellular biosynthetic process / regulation of primary metabolic process / positive regulation of DNA-templated transcription initiation / SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA polymerase II preinitiation complex assembly / DNA-templated transcription initiation / chromatin organization / RNA polymerase II-specific DNA-binding transcription factor binding / molecular adaptor activity / protein heterodimerization activity / chromatin binding / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytosol
Similarity search - Function
LisH / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor TFIID component TAF4, C-terminal / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TAFII31 ...LisH / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor TFIID component TAF4, C-terminal / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TAFII31 / TAF6, C-terminal HEAT repeat domain superfamily / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 12 domain / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAF6 C-terminal HEAT repeat domain / TAF6, C-terminal HEAT repeat domain / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Aminopeptidase N-like , N-terminal domain superfamliy / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Subunit (60 kDa) of TFIID and SAGA complexes / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 2 / TBP-associated factor 4 / Transcription initiation factor TFIID subunit 5
Similarity search - Component
Biological speciesKomagataella phaffii GS115 (fungus)
Komagataella phaffii (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsKolesnikova, O. / Ben-Shem, A. / Luo, J. / Ranish, J. / Schultz, P. / Papai, G.
Funding support United States, France, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P50 GM076547 RO1 GM110064 United States
French National Research AgencyANR-15-CE11-0022-01 France
French National Research AgencyANR-10-LABX-0030-INRT France
CitationJournal: Nat Commun / Year: 2018
Title: Molecular structure of promoter-bound yeast TFIID.
Authors: Olga Kolesnikova / Adam Ben-Shem / Jie Luo / Jeff Ranish / Patrick Schultz / Gabor Papai /
Abstract: Transcription preinitiation complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) ...Transcription preinitiation complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. Here we present the cryo-electron microscopy structure of promoter-bound yeast TFIID at a resolution better than 5 Å, except for a flexible domain. We position the crystal structures of several subunits and, in combination with cross-linking studies, describe the quaternary organization of TFIID. The compact tri lobed architecture is stabilized by a topologically closed Taf5-Taf6 tetramer. We confirm the unique subunit stoichiometry prevailing in TFIID and uncover a hexameric arrangement of Tafs containing a histone fold domain in the Twin lobe.
History
DepositionSep 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Category: em_imaging_optics / Item: _em_imaging_optics.phase_plate
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: Taf2
B: Subunit (90 kDa) of TFIID and SAGA complexes
C: Subunit (90 kDa) of TFIID and SAGA complexes
D: Subunit (60 kDa) of TFIID and SAGA complexes
E: Subunit (60 kDa) of TFIID and SAGA complexes
F: Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation
G: Taf8
I: Histone-fold
H: Histone-fold
K: Subunit (61/68 kDa) of TFIID and SAGA complexes
J: TFIID subunit (48 kDa)


Theoretical massNumber of molelcules
Total (without water)634,42911
Polymers634,42911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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Protein , 9 types, 11 molecules ABCDEFGIHKJ

#1: Protein Taf2


Mass: 199179.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / References: UniProt: C4R289*PLUS
#2: Protein Subunit (90 kDa) of TFIID and SAGA complexes


Mass: 80933.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4R4L4
#3: Protein Subunit (60 kDa) of TFIID and SAGA complexes


Mass: 54888.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4QW33
#4: Protein Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation


Mass: 17303.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4QZS5
#5: Protein Taf8


Mass: 6400.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus)
#6: Protein Histone-fold


Mass: 5464.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus)
#7: Protein Histone-fold


Mass: 5805.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus)
#8: Protein Subunit (61/68 kDa) of TFIID and SAGA complexes


Mass: 66690.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4R150
#9: Protein TFIID subunit (48 kDa) / Transcription factor II D


Mass: 61942.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
References: UniProt: C4R420

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Transcription Factor IIDTranscription factor II D / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.9 MDa / Experimental value: NO
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
Buffer solutionpH: 8
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Calibrated magnification: 45454 X / Nominal defocus max: 3800 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 4900 nm / Cs: 0.01 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 52.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV / Spherical aberration corrector: Equipped with Cs corrector
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 3-40

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Processing

EM software
IDNameCategory
1Gautomatchparticle selection
2SerialEMimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 295734
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180823 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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